With the single-nerve fiber action potential recording method and the single-motor unit electromyography, the functioning of the human central nervous system (CNS) is analysed at the single-neuron level under physiologic conditions following injury, malformation and degeneration. It is shown that the self-organisation of the neuronal networks of the human CNS by phase and frequency coordination becomes impaired following all nervous system diseases. Out of the differences between the functioning of the healthy and pathologically functioning CNS, a repair treatment is developed called Co-ordination Dynamics Therapy (CDT). This movement-based learning therapy is able to improve almost every nervous system in its functioning by functional and structural repair for all ages including premature born babies and in aging. The therapy progress with CDT can be quantified by using the System Theory of Pattern Formation. By pattern change, given by a special CDT device, a single value is obtained for the quality of CNS functioning. Especially the tremor in Parkinson's disease and the urinary bladder repair in spinal cord injury are analysed in detail by the human neurophysiologic recording methods and clinical assessments. The repair of the human nervous system is shown in cross-sectional and longitudinal studies in mild and severe traumatic brain and spinal cord injuries. By applying CDT, CNS functioning can also be improved in Parkinson's disease and in aging. The rate of improvement/repair by learning is measured in the healthy and the diseased nervous systems. It is emphasised that the efficacy of movement-based learning therapies may differ by a factor of 100. A powerful tool in learning is the learning transfer. By training integrative movements, including automatisms, not only the trained movements can be improved, but also the vegetative and higher mental functions can be repaired as, for example, continence, speech and cardiovascular performance.